Contacts of the helix formed by residues 309 - 325 (chain A) in PDB entry 4C3P
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with LYS 309 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306A HIS* 2.7 42.2 + - + +
308A GLU* 1.3 79.1 - - + +
310A VAL* 1.3 63.5 + - - -
311A ASP 3.1 2.2 - - - -
312A LEU* 3.0 30.2 + - + +
368A PRO* 3.8 27.1 - - + +
369A SER* 4.6 6.1 + - - +
371A ARG* 3.0 34.0 + - + +
372A PRO 3.0 27.7 + - - +
373A MET* 3.8 17.1 - - - +
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Residues in contact with VAL 310 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253A ILE* 4.9 3.4 - - + -
255A ARG* 4.5 25.6 - - + +
306A HIS 3.7 1.0 + - - +
307A ASP* 2.9 27.8 + - + +
309A LYS* 1.3 78.6 - - - +
311A ASP* 1.3 65.4 + - - +
312A LEU 3.1 1.1 + - - -
313A TRP* 3.3 12.0 + - - +
314A SER* 3.5 10.7 + - - +
371A ARG* 3.8 8.5 - - - +
297D PRO* 3.4 23.3 - - + -
299D GLU* 3.6 17.0 - - + +
300D MET* 4.1 29.6 - - + -
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Residues in contact with ASP 311 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244A LEU* 3.5 24.7 - - + +
248A HIS* 2.5 42.4 + - + +
253A ILE* 3.7 5.8 - - - +
254A HIS* 2.3 43.4 + - - +
255A ARG* 4.2 5.4 - - - +
257A ILE* 4.8 3.3 - - - +
308A GLU 3.4 1.4 + - - +
309A LYS 3.1 1.4 - - - -
310A VAL* 1.3 77.7 - - - +
312A LEU* 1.3 62.6 + - + +
313A TRP 3.4 0.2 - - - -
314A SER* 3.8 6.7 + - - -
315A LEU* 3.4 27.4 + - - +
374A LEU* 5.7 0.4 - - + -
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Residues in contact with LEU 312 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248A HIS* 5.6 1.6 - - + -
308A GLU* 5.0 4.7 - - + +
309A LYS* 3.0 30.4 + - + +
311A ASP* 1.3 78.2 - - - +
313A TRP* 1.3 67.3 + - - +
315A LEU* 3.4 4.5 + - + +
316A GLY 3.2 13.3 + - - -
363A LEU* 3.4 41.4 - - + +
371A ARG* 4.2 13.5 - - + -
372A PRO* 3.3 26.9 - - + +
373A MET* 4.2 7.9 - - - -
374A LEU* 3.9 26.7 - - + -
375A ARG* 5.8 2.0 - - - +
377A VAL* 3.7 20.9 - - + -
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Residues in contact with TRP 313 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309A LYS 3.7 2.8 + - - -
310A VAL 3.3 10.2 + - - +
312A LEU* 1.3 76.2 - - - +
314A SER* 1.3 55.1 + - - +
316A GLY* 2.7 24.9 + - - -
317A VAL* 2.9 31.7 + - + +
329A PHE* 3.6 33.0 - + - -
341A ILE* 3.9 15.9 - - + +
344A VAL* 4.1 14.1 - - + -
363A LEU 3.9 9.3 + - - -
364A LEU* 3.6 34.7 - - + +
365A LYS 3.6 25.4 - - - -
371A ARG* 3.9 23.5 - - - +
294D ASP 5.1 0.8 + - - -
295D TYR 4.0 7.9 + - - -
296D LEU 3.6 11.1 + - - -
297D PRO* 3.7 25.4 - - + -
298D PRO* 3.8 17.9 - - + -
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Residues in contact with SER 314 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255A ARG 3.6 18.0 + - - -
257A ILE* 4.2 31.8 + - - +
310A VAL* 3.5 11.6 + - - +
311A ASP* 3.8 11.1 - - - -
313A TRP* 1.3 82.5 - - - +
315A LEU* 1.3 63.5 + - - -
316A GLY 3.1 0.2 + - - -
317A VAL* 3.2 5.4 + - - +
318A LEU* 2.9 29.6 + - - +
295D TYR* 4.0 14.2 + - - -
297D PRO* 5.4 0.7 - - - +
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Residues in contact with LEU 315 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237A ILE* 3.9 31.2 - - + +
240A LEU* 4.5 17.9 - - + -
241A ALA* 4.1 15.7 - - + -
244A LEU* 3.2 34.3 - - + -
257A ILE* 5.5 1.1 - - + -
311A ASP 3.4 14.5 + - - +
312A LEU* 3.4 11.3 + - + +
313A TRP 3.3 0.8 - - - -
314A SER* 1.3 77.0 - - - +
316A GLY* 1.3 57.1 - - - +
318A LEU* 3.9 5.7 - - + +
319A CYS* 2.9 32.6 + - - +
363A LEU* 4.1 8.3 - - + -
374A LEU* 4.4 10.1 - - + -
377A VAL* 3.9 22.4 - - + -
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Residues in contact with GLY 316 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312A LEU 3.2 3.6 + - - -
313A TRP 2.7 14.3 + - - -
315A LEU* 1.3 76.4 - - - +
317A VAL* 1.3 61.6 + - - -
319A CYS* 3.6 3.3 - - - +
320A TYR* 3.0 22.2 + - - +
360A ILE* 4.0 6.9 - - - +
363A LEU* 3.6 28.9 - - - -
364A LEU* 3.8 11.9 - - - -
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Residues in contact with VAL 317 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313A TRP* 2.9 44.6 + - + +
314A SER* 3.7 8.1 - - - +
316A GLY* 1.3 75.3 - - - +
318A LEU* 1.3 57.0 + - - +
320A TYR* 3.1 4.7 + - - +
321A GLU* 2.9 25.3 + - - +
327A PRO* 4.4 2.5 - - + -
328A PRO* 4.0 21.3 - - + +
329A PHE* 4.4 10.1 - - + -
364A LEU* 3.5 9.8 - - + +
294D ASP 4.0 12.8 - - - +
295D TYR* 3.6 33.9 - - + +
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Residues in contact with LEU 318 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237A ILE* 4.9 2.9 - - + -
240A LEU* 4.0 21.8 - - + -
257A ILE* 3.9 34.8 - - + +
259A PRO* 3.8 28.3 - - + -
262A LEU* 4.1 10.1 - - + -
314A SER 2.9 22.0 + - - +
315A LEU* 3.9 4.7 - - + +
317A VAL* 1.3 74.1 - - - +
319A CYS* 1.3 57.4 + - - +
321A GLU* 2.9 7.6 + - - +
322A PHE* 2.7 76.5 + - + -
295D TYR* 4.9 3.8 - - + -
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Residues in contact with CYS 319 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233A THR* 3.9 21.1 - - - -
237A ILE* 3.6 21.8 - - + +
315A LEU 2.9 19.0 + - - +
316A GLY* 3.6 5.4 - - - +
318A LEU* 1.3 77.0 - - - +
320A TYR* 1.3 63.0 + - - +
322A PHE* 3.3 2.8 + - - +
323A LEU* 3.2 23.6 + - - +
356A ALA* 5.6 0.9 - - - -
359A LEU* 5.0 6.5 - - + -
360A ILE* 3.9 23.8 - - + -
363A LEU* 5.4 3.4 - - + -
382A TRP* 4.1 20.9 - - - -
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Residues in contact with TYR 320 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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316A GLY 3.0 13.4 + - - +
317A VAL 3.2 8.3 - - - +
319A CYS* 1.3 78.6 - - - +
321A GLU* 1.3 61.4 + - - +
323A LEU* 3.3 2.9 + - - -
324A VAL* 3.0 44.5 + - + +
326A LYS* 3.2 26.5 + - - -
327A PRO 3.8 0.9 - - - -
328A PRO* 3.3 47.1 + - + +
346A PHE* 4.4 7.6 - + + -
347A THR 2.9 24.2 + - - -
348A PHE* 3.9 35.9 - + - -
349A PRO* 4.1 7.3 - - + +
360A ILE* 4.1 18.6 - - + +
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Residues in contact with GLU 321 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219A TYR* 5.6 4.0 - - - -
222A LEU* 4.0 16.3 - - + +
259A PRO* 3.4 19.9 - - - +
317A VAL 2.9 13.8 + - - +
318A LEU* 2.9 8.4 + - - +
320A TYR* 1.3 75.2 - - - +
322A PHE* 1.3 61.1 + - + +
325A GLY* 2.6 34.0 + - - +
326A LYS* 3.7 29.7 - - - +
327A PRO* 4.2 14.4 - - + +
295D TYR* 2.4 42.2 + - - -
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Residues in contact with PHE 322 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218A VAL* 3.9 28.0 - - + -
222A LEU* 4.1 13.5 - - + -
227A LYS* 3.6 4.5 - - - +
228A PHE* 3.0 48.0 + + + -
233A THR* 3.4 32.1 - - + +
236A TYR* 3.8 27.6 - + + -
237A ILE* 4.3 15.9 - - + -
240A LEU* 4.8 3.4 - - + -
259A PRO* 4.7 1.8 - - + -
262A LEU* 4.1 9.6 - - + -
318A LEU* 2.7 51.3 + - + +
319A CYS 3.6 4.3 - - - +
321A GLU* 1.3 77.1 - - + +
323A LEU* 1.3 58.6 + - - +
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Residues in contact with LEU 323 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227A LYS* 3.2 21.7 + - - +
228A PHE 4.0 11.7 - - - +
230A GLU* 4.3 19.3 - - + -
233A THR* 3.3 28.3 - - + +
319A CYS* 3.2 22.6 + - - +
320A TYR* 4.0 3.4 - - - +
322A PHE* 1.3 76.6 - - - +
324A VAL* 1.3 63.9 + - + +
351A PHE* 3.7 15.1 - - + -
352A VAL* 4.3 16.2 - - + -
356A ALA* 3.8 28.5 - - + -
360A ILE* 4.2 14.4 - - + -
382A TRP* 4.3 6.3 - - + -
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Residues in contact with VAL 324 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227A LYS* 4.1 12.0 - - - +
320A TYR* 3.0 43.0 + - + +
323A LEU* 1.3 82.9 - - + +
325A GLY* 1.3 61.6 + - - +
326A LYS* 3.3 36.8 - - + +
349A PRO* 3.9 31.6 - - + -
351A PHE* 4.6 7.6 - - + -
352A VAL* 4.1 13.7 - - + -
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Residues in contact with GLY 325 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222A LEU* 4.6 5.6 - - - +
226A SER 3.3 25.6 - - - +
227A LYS* 4.2 1.1 - - - +
321A GLU* 2.6 27.1 + - - +
323A LEU 3.7 1.0 - - - -
324A VAL* 1.3 74.0 - - - +
326A LYS* 1.3 63.9 + - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il